Variant report

Variant	rs2296724
Chromosome Location	chr14:69820946-69820947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69820575..69822363-chr14:69824777..69827563,2	MCF-7	breast:
2	chr14:69800242..69802795-chr14:69820027..69823716,5	MCF-7	breast:
3	chr14:69819465..69821642-chr14:69923369..69926196,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10083335	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10129186	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10138313	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10140273	0.93[EUR][1000 genomes]
rs10142144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10143593	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10151691	0.88[ASW][hapmap];0.82[TSI][hapmap]
rs11622711	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11623094	0.87[TSI][hapmap]
rs11624577	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12878175	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12884348	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12893282	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12895620	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1958121	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2085193	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2124191	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296722	0.88[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296727	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28401542	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28470369	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28661733	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34450502	0.92[EUR][1000 genomes]
rs34731892	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34834622	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34840252	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3759770	0.87[TSI][hapmap]
rs3759771	0.96[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4899294	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4899295	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4902717	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56137363	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56953348	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58553067	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67502261	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7143858	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7145944	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7147362	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7147710	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7150586	0.87[TSI][hapmap]
rs8012954	0.96[CEU][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8014890	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8015317	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8015425	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8016781	0.96[CEU][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs959242	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456334	chr14:69793624-69831037	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv564966	chr14:69793624-69831037	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2296724	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL
rs2296724	EXD2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69793400-69821200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr14:69793400-69822600	Weak transcription	Brain Angular Gyrus	brain
3	chr14:69800800-69821800	Weak transcription	Brain Hippocampus Middle	brain
4	chr14:69807000-69821000	Weak transcription	Fetal Intestine Large	intestine
5	chr14:69808600-69821600	Weak transcription	Brain Anterior Caudate	brain
6	chr14:69809800-69822800	Weak transcription	Right Atrium	heart
7	chr14:69810200-69821600	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:69810200-69822000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr14:69812200-69821600	Weak transcription	Aorta	Aorta
10	chr14:69813400-69821000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:69815400-69821200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:69815600-69821200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:69815600-69838800	Weak transcription	Brain Germinal Matrix	brain
14	chr14:69816400-69821800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr14:69816400-69822200	Weak transcription	Right Ventricle	heart
16	chr14:69817200-69821800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr14:69817600-69822600	Weak transcription	Fetal Stomach	stomach
18	chr14:69817600-69823000	Enhancers	Primary B cells from peripheral blood	blood
19	chr14:69817800-69821000	Enhancers	GM12878-XiMat	blood
20	chr14:69818200-69821800	Weak transcription	Adipose Nuclei	Adipose
21	chr14:69818400-69821200	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr14:69818400-69822200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:69818400-69827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr14:69818600-69842800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr14:69818800-69821000	Strong transcription	Fetal Brain Female	brain
26	chr14:69819000-69821000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:69819000-69822400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:69819200-69822400	Weak transcription	Left Ventricle	heart
29	chr14:69819600-69821000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:69820400-69821000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:69820400-69821000	Enhancers	Duodenum Mucosa	Duodenum
32	chr14:69820400-69823000	Enhancers	Primary B cells from cord blood	blood
33	chr14:69820600-69821000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:69820600-69821000	Enhancers	Colonic Mucosa	Colon
35	chr14:69820600-69821200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr14:69820600-69821200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr14:69820600-69821200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:69820600-69821200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr14:69820600-69821200	Enhancers	Spleen	Spleen
40	chr14:69820600-69821400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:69820600-69821400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr14:69820600-69822000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:69820600-69822000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr14:69820600-69822800	Enhancers	Fetal Thymus	thymus
45	chr14:69820600-69823000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr14:69820800-69821000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr14:69820800-69821000	Genic enhancers	Fetal Intestine Small	intestine
48	chr14:69820800-69821000	Enhancers	HSMMtube	muscle
49	chr14:69820800-69821200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr14:69820800-69821200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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